Molecular docking towards drug discovery

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Abstract
Fueled by advances in molecular structure determination, tools for structure-based drug design are proliferating rapidly. Lead discovery through searching of ligand databases with molecular docking techniques represents an attractive alternative to high-throughput random screening. The size of commercial databases imposes severe computational constraints on molecular docking, compromising the level of calculational detail permitted for each putative ligand. We describe alternative philosophies for docking which effectively address this challenge. With respect to the dynamic aspects of molecular recognition, these strategies lie along a spectrum of models bounded by the Lock-and-Key and Induced-Fit theories for ligand binding. We explore the potential of a rigid model in exploiting species specificity and of a tolerant model in predicting absolute ligand binding affinity. Current molecular docking methods are limited primarily by their ability to rank docked complexes; we therefore place particular emphasis on this aspect of the problem throughout our validation of docking strategies.